South Africa has the third highest annual number of new tuberculosis (TB) cases globally. The resurgence of TB which has particularly affected gold miners in South Africa, is attributed to occupational risk factors for TB including silica dust exposure and high HIV prevalence. Isoniazid preventive therapy (IPT) is recommended for individuals at high risk to prevent both HIV-related TB and silicotuberculosis, but global uptake has been poor. We describe the design of a cluster randomised study, "Thibela TB", which compares routine IPT targeted to those identified as at higher risk of TB (due to HIV infection or silicosis) against a "community-wide" approach in which IPT is offered to all employees. The trial is registered with the Current Controlled Trials: Registration number ISRCTN63327174.